Your BIOS is already installed. Do you need to download the BIOS on ASUS' website in order to update the version? Simply check your BIOS version during the POST screen and compare it to the BIOS version offered on ASUS' website.
Your BIOS doesn't change during a clean install. It's stored in a ROM chip, whereas all your drivers are located on your C: drive. Typically, C:\WINDOWS\system32\Drivers. Since you essentially wipe your C:\ drive clean during a clean install, all your drivers are eliminated, and thus, you need to reinstall them.
Regarding the PCI Simple Communications Controller, this website states,
PCI stands for Peripheral Component Interconnect and is an industry standard bus for attaching peripheral devices to a computer. The PCI Simple Communications Controller is a generic label given by Windows to PCI boards installed in a PC when the drivers for the device are not installed.
So, the question is, do you have something installed in one of the PCI slots on your motherboard? If so, you need to install its driver.
Please use the hyperlinked website to further investigate your problem, as it offers more solutions that may benefit you.